Merge pull request #913 from oliverdutton/master

Fix: OPS hangs when external engine errors/exits unexpectedly

openpathsampling/engines/dynamics_engine.py

@@ -95,7 +95,7 @@ class DynamicsEngine(StorableNamedObject):
         some trajectory you might not restart completely. Possibilities are
 
         1.  `full` will restart completely and use the initial frames (default)
-        2.  `50%` will cut the existing in half but keeping at least the initial
+        2.  `keep_half` will cut the existing in half but keeping at least the initial
         3.  `remove_interval` will remove as many frames as the `interval`
         4.  a callable will be used as a function to generate the new from the
             old trajectories, e.g. `lambda t: t[:10]` would restart with the
@@ -509,15 +509,17 @@ def iter_generate(self, initial, running=None, direction=+1,
                             int(len(trajectory) * 0.9),
                             max(
                                 len(initial),
-                                len(trajectory) / 2))]
+                                int(len(trajectory) / 2)))]
                 elif hasattr(self.on_retry, '__call__'):
                     trajectory = self.on_retry(trajectory)
-
-            if direction > 0:
-                self.current_snapshot = trajectory[-1]
-            elif direction < 0:
-                # backward simulation needs reversed snapshots
-                self.current_snapshot = trajectory[0].reversed
+
+            """ Case of run dying before first output"""
+            if len(trajectory) >= 1:
+                if direction > 0:
+                    self.current_snapshot = trajectory[-1]
+                elif direction < 0:
+                    # backward simulation needs reversed snapshots
+                    self.current_snapshot = trajectory[0].reversed
 
             logger.info("Starting trajectory")
             self.start()

openpathsampling/engines/external_engine.py

@@ -210,11 +210,11 @@ def generate_next_frame(self):
             #print self.frame_num, next_frame # DEBUG LOGGER
             now = time.time()
             if next_frame == "partial":
-                if not self.proc.is_running():
+                if self.proc.poll() is not None:
                     raise RuntimeError("External engine died unexpectedly")
                 time.sleep(0.001) # wait a millisec and rerun
             elif next_frame is None:
-                if not self.proc.is_running():
+                if self.proc.poll() is not None:
                     raise RuntimeError("External engine died unexpectedly")
                 logger.debug("Sleeping for {:.2f}ms".format(self.sleep_ms))
                 time.sleep(self.sleep_ms/1000.0)
@@ -265,10 +265,13 @@ def stop(self, trajectory):
         proc = self.who_to_kill()
         logger.info("About to send signal %s to %s", str(self.killsig),
                     str(proc))
-        proc.send_signal(self.killsig)
-        logger.debug("Signal has been sent")
-        proc.wait()  # wait for the zombie to die
-        logger.debug("Zombie should be dead")
+        try:
+            proc.send_signal(self.killsig)
+            logger.debug("Signal has been sent")
+            proc.wait()  # wait for the zombie to die
+            logger.debug("Zombie should be dead")
+        except psutil.NoSuchProcess:
+            logger.debug("Tried to kill process, but it was already dead")
         self.cleanup()
 
     # FROM HERE ARE THE FUNCTIONS TO OVERRIDE IN SUBCLASSES:

openpathsampling/engines/gromacs/engine.py

@@ -117,6 +117,10 @@ class GromacsEngine(ExternalEngine):
               -e self.edr_file -g self.log_file``, where the ``topol.top``
               is generated by :meth:`.prepare`, and the other filenames are
               set by :meth:`.set_filenames`. Default is the empty string.
+            * ``snapshot_timestep``: time between frames analysed by ops. 
+              You keep track of the unit, I'd advise ps so the output
+              rates will be in ps. Example. 2 fs timestep in the mdp with 
+              nstxout of 30 would give snapshot_timestep of 60 fs = 0.06 ps
 
     base_dir : string
         root directory where all files will be found (defaults to pwd)
@@ -127,7 +131,8 @@ class GromacsEngine(ExternalEngine):
         **{
             'gmx_executable': "gmx ",
             'grompp_args': "",
-            'mdrun_args': ""
+            'mdrun_args': "",
+            'snapshot_timestep':1.0
         }
     )
     GROMPP_CMD = ("{e.options[gmx_executable]}grompp -c {e.gro} "
@@ -278,9 +283,9 @@ def write_frame_to_file(self, filename, snapshot, mode='w'):
         xyz = np.asarray([snapshot.xyz], dtype=np.float32)
         time = np.asarray([0.0], dtype=np.float32)
         step = np.asarray([0], dtype=np.int32)
-        box = np.asarray([snapshot.box_vectors], dtype=np.float32)
+        box = np.asarray([np.asarray(snapshot.box_vectors)], dtype=np.float32)
         lambd = np.asarray([0.0], dtype=np.float32)
-        vel = np.asarray([snapshot.velocities], dtype=np.float32)
+        vel = np.asarray([np.asarray(snapshot.velocities)], dtype=np.float32)
 
         try:
             trr = TRRTrajectoryFile(filename, mode)

openpathsampling/engines/toy/__init__.py

@@ -1,6 +1,6 @@
 from .integrators import (LangevinBAOABIntegrator, LeapfrogVerletIntegrator)
 from .pes import Gaussian, HarmonicOscillator, LinearSlope, OuterWalls, \
-    PES_Add, PES_Combination, PES_Sub, PES
+    PES_Add, PES_Combination, PES_Sub, PES, BolhuisExample
 
 from .engine import ToyEngine as Engine
 from .engine import ToyEngine

openpathsampling/engines/toy/pes.py

@@ -368,3 +368,54 @@ def dVdx(self, sys):
         """
         # this is independent of the position
         return self._local_dVdx
+
+class BolhuisExample(PES):
+    r"""Creates an x**4 - 2 x**2 1 dimensional PES
+
+    Parameters
+    ----------
+    None
+    """
+    def __init__(self):
+        super(BolhuisExample, self).__init__()
+        self._local_dVdx = np.zeros(1)
+
+    def __repr__(self):  # pragma: no cover
+        return "The x**4 - 2 x**2 example in Bolhuis papers potential"
+
+    def V(self, sys):
+        """Potential energy
+
+        Parameters
+        ----------
+        sys : :class:`.ToyEngine`
+            engine contains its state, including velocities and masses
+
+        Returns
+        -------
+        float
+            the potential energy
+        """
+        dx = sys.positions
+        myV = 0.0
+        for i in range(len(dx)):
+            myV += dx[i]**4 - 2 * dx[i]**2
+        return myV
+
+    def dVdx(self, sys):
+        """Derivative of potential energy (-force)
+
+        Parameters
+        ----------
+        sys : :class:`.ToyEngine`
+            engine contains its state, including velocities and masses
+
+        Returns
+        -------
+        np.array
+            the derivatives of the potential at this point
+        """
+        dx = sys.positions
+        for i in range(len(dx)):
+            self._local_dVdx[i] =4*dx[i]**3 - 4*dx[i]
+        return self._local_dVdx